Analysis of RNA polymerase by trypsin cleavage. Evidence for a specific association between subunits sigma and beta involved in the closed to open complex transition

Equivalence of Mg2+ and Na+ ions in salt dependence of the equilibrium binding and dissociation rate constants of Escherichia coli RNA polymerase open complex

Conflicting experimental data on the influence of Mg(2+) ions on the salt dependence of formation/dissociation of open transcription complex (RPo) of Escherichia coli RNA polymerase led us to carry systematic measurements of the dissociation rate constant (k(d)) and thermodynamic stability of complexes at lambdaP(R) and Pa promoters in a broad range of [NaCl] and [MgCl(2)] at 25, 31 and 37 degrees C, using fluorescence detected abortive transcription assay. Values of k(d) determined in MgCl(2) in the presence of heparin, as a commonly used anionic competitor, were shown to depend on heparin concentration whereas in NaCl this effect was not observed. Kinetics of dissociation was therefore determined in the course of salt-induced down-shift of the binding equilibrium. Salt derivatives of k(d)'s (n(d)) appeared to be similar in NaCl (approximately 8.5) and MgCl(2) (approximately 10) for both complexes. Isotherms of fractional occupancy of promoters by RNAP as a function of ln [salt] were shown to conform to a sigmoid Boltzman function parameterized to include binding constant of RPo and a net change (n(obs)) in the number of electrolyte ions associated with complex components upon its formation/dissociation. The fitted values of n(obs) appeared also similar in NaCl and in MgCl(2): approximately 18 for RPo/lambdaP(R) and approximately 20 for RPo/Pa, respectively. Overall unfavorable vant'Hoff enthalpy (DeltaH(obs)) of RPo proved to be much higher in MgCl(2) than in NaCl by ca. 20 kcal/mol for both complexes, rendering them profoundly less stable in the former salt. In both salts, DeltaH(obs) was higher by approximately 30 kcal/mol for RPo/Pa relative to RPo/lambdaP(R). Similarity of n(obs) and n(d) values for the two salts indicates thermodynamic equivalence of Mg(2+) and Na(+) in [salt]-controlled binding equilibrium of RPo. This finding remains in disagreement with earlier data and suggests that salt effects on open complex stability should be sought in global compensating changes in distribution of all ionic species around the interacting complex components.

A Hydrophobic Patch on the Flap-tip Helix of E.coli RNA Polymerase Mediates σ70 Region 4 Function

The Escherichia coli RNA polymerase beta subunit contains a flexible flap domain that interacts with region 4 of sigma(70) to position it for recognition of the -35 element of promoters. We report that this function depends on a hydrophobic patch on one face of the short stretch of alpha helix located at the tip of the flap domain, called the flap-tip helix. Disruption of the hydrophobic patch by the substitution of hydrophilic or charged amino acids resulted in a loss of the interaction between the flap and sigma region 4, as determined by protease sensitivity assays, and impaired transcription from -35-dependent promoters. We suggest that contact of the flap-tip helix hydrophobic patch to the sigma region 4 hydrophobic core is essential for stable interaction of the flap-tip helix with region 4. This contact allowed region 4.2 recognition of the -35 promoter element and appeared to stabilize region 4 interaction with the beta' Zn(2+) binding domain. Our studies failed to detect any role for sigma region 1.1 in establishing or maintaining the flap-sigma region 4 interaction, consistent with recent reports placing sigma region 1.1 in the downstream DNA channel.

The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription

The sigma(70) subunit of Escherichia coli RNA polymerase (RNAP) is a transcription initiation factor that can also be associated with RNAP during elongation. We provide biochemical evidence that sigma(70) induces a transcription pause at the lacUV5 promoter after RNAP has synthesized a 17-nucleotide transcript. The sigma(70)-dependent pausing requires an interaction between sigma(70) and a part of the lac repressor operator sequence resembling a promoter -10 consensus. The polysaccharide heparin triggers the release of sigma(70) from the paused complexes, supporting the view that during the transition from initiation to elongation the interactions between sigma(70) and core RNAP are weakened. We propose that the binding and retention of sigma(70) in elongation complexes are stabilized by its ability to form contacts with DNA of the transcription bubble. In addition, we suggest that the sigma(70) subunit in the elongation complex may provide a target for regulation of gene expression.

Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process

The interaction of RNA polymerase and its initiation factors is central to the process of transcription initiation. To dissect the role of this interface, we undertook the identification of the contact sites between RNA polymerase and sigma(70), the Escherichia coli initiation factor. We identified nine mutationally verified interaction sites between sigma(70) and specific domains of RNA polymerase and provide evidence that sigma(70) and RNA polymerase interact in at least a two-step process. We propose that a cycle of changes in the interface of sigma(70) with core RNA polymerase is associated with progression through the process of transcription initiation.

How sigma docks to RNA polymerase and what sigma does

It is clear that multiple sites of interaction exist between sigmas and core subunits, likely reflecting the changing pattern of interactions that occur sequentially during the complex process of holoenzyme formation, open promoter formation, and initiation of transcription. Recent studies have revealed that a major site of interaction of Escherichia coli sigma factors is the amino acid 260-309 coiled-coil region of the beta' subunit of core RNA polymerase. This region of beta' interacts with region 2.1-2.2 of sigma(70). Binding of this region of beta' to sigma(70) triggers a conformational change in sigma that allows it to bind to a -10 nontemplate promoter DNA strand oligonucleotide.

Structural and functional properties of a Bacillus subtilis temperature-sensitive sigma(A) factor

Bacillus subtilis DB1005 is a temperature-sensitive (Ts) sigA mutant containing double-amino-acid substitutions (I198A and I202A) on the hydrophobic face of the promoter -10 binding helix of sigma(A) factor. We have analyzed the structural and functional properties of this mutant sigma(A) factor both in vivo and in vitro. Our data revealed that the Ts sigma(A) factor possessed predominantly a multimeric structure which was prone to aggregation at restrictive temperature. The extensive aggregation of the Ts sigma(A) resulted in a very low core-binding activity of the Ts sigma(A) factor and a markedly reduced sigma(A)-RNA polymerase activity in B. subtilis DB1005, suggesting that extensive aggregation of the Ts sigma(A) is the main trigger for the temperature sensitivity of B. subtilis DB1005. Partial proteolysis, tryptophan fluorescence and 1-anilinonaphthalene-8-sulfonate-binding analyses revealed that the hydrophobic face of the promoter -10 binding helix and also the hydrophobic core region of the Ts sigma(A) factor were readily exposed on the protein surface. This hydrophobic exposure provides an important cue for mutual interaction between molecules of the Ts sigma(A) and allows the formation of multimeric Ts sigma(A). Our results also indicate that Ile-198 and Ile-202 on the hydrophobic face of the promoter -10 binding helix are essential to ensure the correct folding and stabilization of the functional structure of sigma(A) factor.

Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase

In eubacteria, the final sigma subunit binds to the core RNA polymerase and directs transcription initiation from any of its cognate set of promoters. Previously, our laboratory defined a region of the beta' subunit that interacts with final sigma(70) in vitro. This region of beta' contained heptad repeat motifs indicative of coiled coils. In this work, we used 10 single point mutations of the predicted coiled coils, located within residues 260-309 of beta', to look at disruption of the final sigma(70)-core interaction. Several of the mutants were defective for binding final sigma(70) in vitro. Of these mutants, three (R275Q, E295K, and A302D) caused cells to be inviable in an in vivo assay in which the mutant beta' is the sole source of beta' subunit for the cell. All of the mutants were able to assemble into the core enzyme; however, R275Q, E295K, A302D were defective for Efinal sigma(70) holoenzyme formation. Several of the mutants were also defective for holoenzyme assembly with various minor final sigma factors. In the recently published crystal structure of Thermus aquaticus core RNA polymerase (Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K. , and Darst, S. A. (1999) Cell 98, 811-824), the region homologous to beta'(260-309) of Escherichia coli forms a coiled coil. Modeling of our mutations onto that coiled coil places the most defective mutations on one face of the coiled coil.

Human adenovirus serotype 3 (Ad3) and the Ad3 fiber protein bind to a 130-kDa membrane protein on HeLa cells

The fiber protein of adenovirus mediates the interaction of adenovirus with cell membrane receptors. We have produced the Ad3 fiber protein in the baculovirus expression system. Biochemical, morphological and functional analyses showed that the recombinant fiber was properly folded and functionally competent. The specific binding of Ad3 virus to two HeLa membrane proteins of 130 and 100 kDa was demonstrated with an overlay protein binding assay. In the same assay, Ad3 fiber only recognized the 130-kDa protein. Divalent cations seemed to be important for the interaction of both virus and fiber with these proteins.

Analysis of wheat-germ RNA polymerase II by trypsin cleavage. The integrity of the two largest subunits of the enzyme is not mandatory for basal transcriptional activity

When wheat-germ RNA polymerase II is subjected to mild proteolytic attack in the presence of trypsin, the resulting form of the enzyme migrates as a single species on electrophoresis in native polyacrylamide gels, with an apparent Mr significantly smaller than that of the native enzyme. Analysis by denaturing gel electrophoresis of the truncated eukaryotic polymerase revealed that the two largest subunits of the native enzyme, i.e. the 220,000-Mr and 140,000-Mr subunits, were cleaved, giving rise to shorter polypeptide chains of Mr 172,800, 155,000, 143,000, 133,800, 125,000 and 115,000. The use of affinity-purified antibodies directed against each of the two large subunits of the native enzyme allowed us to probe for possible precursor/product relationships between the 220,000-Mr and 140,000-Mr subunits of wheat-germ RNA polymerase II and their breakdown products generated in the presence of trypsin. None of the smaller subunits of the plant RNA polymerase II appeared to be sensitive to trypsin attack. The results indicate that the truncated RNA polymerase retained a multimeric structure, and therefore that the proteolyzed largest subunits of the enzyme remained associated with the smaller ones. Furthermore, in transcription of a poly[d(A-T)] template, the catalytic activity of the proteolyzed form of wheat-germ RNA polymerase II was identical to that of the native enzyme. Therefore, the protein domains that can be deleted by the action of trypsin from the two large subunits of the plant transcriptase are not involved in DNA binding and/or nucleotide binding, and do not play an important role in template-directed catalysis of phosphodiester bond formation.

Adenovirus serotype 3 fibre protein is expressed as a trimer in Escherichia coli

The adenovirus serotype 3 (Ad3) fibre has been expressed in Escherichia coli as an insoluble protein. The protein was solubilized by extraction with urea. Slow removal of urea during the purification procedure resulted in a soluble Ad3 fibre preparation. Polyacrylamide gel analysis of the purified fibre protein, as well as cross-linking experiments performed on cellular debris of expressing cells, suggest that the recombinant Ad3 fibre self-assembles as a trimer from identical polypeptide chains. Gel filtration gave the same exclusion volume for the purified recombinant fibre and for the native fibre in the protein mixture extracted from the Ad3-infected cells. The recombinant fibre was partially resistant to proteolytic degradation, suggesting a folded structure.

Monoclonal antibodies as probes of the topological arrangement of the alpha subunits of Escherichia coli RNA polymerase

Three monoclonal anti-alpha antibodies were used to study the properties of the alpha subunit of Escherichia coli RNA polymerase. None of the monoclonal antibodies inhibited the d(A-T)n-directed synthesis of r(A-U)n. Reassembly of the RNA polymerase core was blocked by mAb 129C4 or mAb 126C6 while no effect was observed with mAb 124D1. The conversion of premature to mature core was partially inhibited by mAb 129C4 and almost totally inhibited by mAb 126C6. The data suggest that during the course of core assembly at least one of the alpha subunits undergoes conformational changes. The increase in affinity of mAb 126C6 for assembled alpha compared with free alpha also implies that alpha undergoes conformational changes during RNA polymerase assembly. Double antibody binding studies showed that the epitopes for mAb 124D1 and mAb 129C4 are available on only one of the alpha subunits in RNA polymerase. It would appear that the relevant domain on one of the alpha subunits in RNA polymerase is well exposed whereas this domain on the second alpha subunit is shielded by interaction with regions of the large beta and beta' subunits. The alpha domain in which the epitope for mAb 126C6 resides is not impeded by subunit interactions in the RNA polymerase. The data obtained also suggest that in the holoenzyme the sigma subunit may be positioned close to one of the alpha subunits, probably to the more exposed alpha. The alpha beta complex is the minimal stable subassembly since one of the alpha subunits dissociates from the alpha 2 beta complex following binding of any of the monoclonal antibodies studied.(ABSTRACT TRUNCATED AT 250 WORDS)

Transcription initiation by Escherichia coli RNA polymerase at the gene II promoter of M13 phage: stability of ternary complex, direct photocrosslinking to nascent RNA, and retention of sigma subunit

The initial stages of transcription have been characterized using a template containing the gene II promoter region of M13 phage. Initiation of transcription in the presence of all four nucleotides gives rise to the 140-residue run-off transcript, with a minor pause at the RNA hexamer stage. Cycling, leading to the accumulation of significant amounts of short oligonucleotides [1], was not observed. An RNA hexamer GUUUUU was the sole product when GpU and UTP were used and the ternary complex with the hexamer was stable and resistant to high salt (0.4 M) and S1 nuclease attack. After direct ultraviolet photocrosslinking of the RNA hexamer to RNA polymerase in the ternary complex, the radioactive label incorporation into various subunits was determined by autoradiography after sodium tetradecyl sulfate gel electrophoresis to be as follows: sigma, 86%; beta, 14%; beta' and alpha, negligible. Both electrophoresis and sucrose gradient centrifugation experiments indicate that the sigma subunit is not released from the ternary complex when either the RNA hexamer or the 140-residue RNA is synthesized on this template, even though the complexes are stable.

Subunit assembly and metabolic stability of E. coli RNA polymerase

Immunological cross-reaction was employed for identification of proteolytic fragments of E. coli RNA polymerase generated both in vitro and in vivo. Several species of partially denatured but assembled RNA polymerase were isolated, which were composed of fragments of the two large subunits, beta and beta', and the two small and intact subunits, alpha and sigma. Comparison of the rate and pathway of proteolytic cleavage in vitro of unassembled subunits, subassemblies, and intact enzymes indicated that the susceptibility of RNA polymerase subunits to proteolytic degradation was dependent on the assembly state. Using this method, degradation in vivo was found for some, but not all, of the amber fragments of beta subunit in merodiploid cells carrying both wild-type and mutant rpoB genes. Although the RNA polymerase is a metabolically stable component in exponentially growing cells of E. coli, degradation of the full-sized subunits was found in two cases, i.e., several temperature-sensitive E. coli mutants with a defect in the assembly of RNA polymerase and the stationary-phase cells of a wild-type E. coli. The in vivo degradation of RNA polymerase was indicated to be initiated by alteration of the enzyme structure.

Structure and function of E. coli promoter DNA

The process of transcription initiation requires both the recognition of a promoter site by RNA polymerase and the melting of a short stretch of DNA. In this review I discuss the properties of promoters that are relevant to sequence recognition and to the ability of the polymerase to act as a melting protein. The regulation of promoter activity is thus dependent on both factors interacting with RNA polymerase and so altering its affinity for promoter sites and also modulations of DNA structure.

Characterization of effects of anti-beta and anti-beta' monoclonal antibodies on the activity of the RNA polymerase from Escherichia coli

Monoclonal antibodies directed against antigenic determinants on the beta and beta' subunits of the Escherichia coli RNA polymerase were characterized by using d(A-T)n-directed transcription assays. Antibodies were prepared by using purified subunits as immunogens, and seven anti-beta and five anti-beta' monoclonal antibodies were generated. Inhibitory anti-beta monoclonal antibodies were found to affect RNA polymerase during synthesis of r(A-U)n, abortive initiation of pApU and UpApU, and elongation by preformed ternary complexes. A comparative enzyme study of r(A-U)n synthesis showed the core polymerase to be more sensitive to inhibition by the anti-beta monoclonal antibody than was the holoenzyme. In contrast, the inhibition effected by the anti-beta' monoclonal antibody was found to be 90% or greater for each of the d(A-T)n-directed assays used. The different inhibitory patterns exhibited by the anti-beta and anti-beta' monoclonal antibodies suggest that the beta and beta' subunits engage in different roles during transcription. Kinetic analysis of the abortive initiation reaction in the presence and absence of the inhibitory antibodies resulted in distinctive but complex modes of inhibition. Inhibition by the anti-beta monoclonal antibody 210E8 was noncompetitive with regard to UTP and competitive for UpA incorporation; at increased UpA concentration, the inhibition was completely reversed. Inhibition of the abortive synthesis of UpApU by the anti-beta' monoclonal antibody 311G2 was noncompetitive with regard to both UpA and UTP incorporation. When the preformed ternary elongation complex was used, inhibition by the anti-beta monoclonal antibody was mixed with regard to the ribonucleoside triphosphate substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of the requirements for transcription pausing in the tryptophan operon

RNA polymerase pausing during transcription of the tryptophan (trp) operon leader region is postulated to be the key event that synchronizes transcription of this region with translation of the coding region for the trp leader peptide. Coupling of transcription to translation enables the cell to monitor the intracellular concentration of charged tRNATrp and determine whether polymerase should terminate transcription at the attenuator or proceed into the structural genes of the operon. We used mutant templates containing deletions of DNA segments corresponding to sequences that are predicted to form alternative RNA secondary structures to show that formation of an RNA hairpin in the leader transcript, and the concentration of the next nucleoside triphosphate to be added to the paused transcript, both markedly affect the kinetics of pausing in vitro. A model is presented that accounts for many of the findings obtained in this and other pausing studies.

Genetic analysis of the tryptophan operon regulatory region using site-directed mutagenesis

The regulatory region of the tryptophan operon of Escherichia coli was subjected to in vitro site-directed mutagenesis using sodium bisulfite as the mutagen. The mutagenized DNA was used to transform cells to drug resistance, and plasmid DNAs from individual transformants were isolated and sequenced. Overall, 22% of the plasmids sequenced contained alterations within the region of interest. Many of the mutants obtained had characteristics that bear on aspects of the alternative secondary structure model of attenuation. Expression analyses with several of the mutants provided evidence suggesting that ribosome dissociation at the leader peptide stop codon may be rapid and that this dissociation is responsible for setting the steady-state level of expression observed in cultures growing in the presence of excess tryptophan. One mutation altered the amino acid composition of the leader peptide without affecting a transcript secondary structure. The behavior of this mutant supports the prediction that the leader peptide per se plays no role in attenuation, rather it is the act of synthesis of the peptide that has regulatory significance. Several of the mutations provide information on the structure of the RNA antiterminator . Additional mutations support the conclusion that the last stem and loop structure in the terminated transcript, structure 3:4, is sufficient to cause transcription termination.

Importance of sodium dodecyl sulfate source to electrophoretic separations of thylakoid polypeptides

Electrophoretic banding patterns of Chlamydomonas reinhardtii thylakoid polypeptides differ depending on whether impure, or pure sodium dodecyl sulfate (SDS) is used. Bands of Mr 45,000 and 36,000 were found when impure sodium dodecyl sulfate was used, but the Mr 45,000 band was absent when pure sodium dodecyl sulfate was used. Seven thylakoid polypeptides were isolated using preparative polyacrylamide gel electrophoresis, and the pure sodium dodecyl sulfate. Polypeptide (Mr 36,000) reran as a single band in pure sodium dodecyl sulfate, but yielded Mr 45,000 and 36,000 bands in impure sodium dodecyl sulfate. Although the Rf of most of the six other polypeptides differed, depending on whether pure or impure sodium dodecyl sulfate was used, the Mr of these polypeptides was the same with both. Thus, the banding pattern difference due to SDS source results from differences in Rf without changes in apparent Mr and a marked change in Mr of one polypeptide.

Overexpression and purification of the sigma subunit of Escherichia coli RNA polymerase

We have constructed a plasmid that overexpresses 100-fold the sigma subunit of Escherichia coli RNA polymerase. The plasmid was constructed by placing the pLoL promoter-operator of bacteriophage lambda upstream from rpoD, the gene encoding the sigma subunit. A simple procedure for purification of the overexpressed protein has been developed based on guanidine hydrochloride denaturation/renaturation, DEAE cellulose chromatography, and Sephacryl S-200 chromatography. The purified product has been characterized and found to be indistinguishable from normally expressed sigma protein purified by previous protocols as judged by enzymatic activity, heat inactivation, and partial proteolysis.

The quaternary structure of Escherichia coli RNA polymerase studied with (scanning) transmission (immuno)electron microscopy

A model for the quaternary structure of Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) is presented. It is based on results from classification of profiles of enzyme molecules, and from application of immuno electron microscopy. Classification of molecules, prepared with the single carbon layer technique, was first achieved for images recorded in dark field with the scanning transmission electron microscope and later on for images recorded in bright-field transmission electron microscopy. It results in five approximately equally sized groups, containing about 80% of the core enzyme profiles. Holoenzyme profiles can be grouped into the same classes, and have approximately the same dimensions (9 nm X 16 nm). Based on the shapes and sizes of the classified profiles, a tentative model for core enzyme has been constructed. Correlation of shadow projections of this model, with the distributions of attachment sites of antibodies against alpha, beta, beta' and sigma over the profiles, has led to models for core and holoenzyme in which the subunits are localized. The model is compared with literature data on the quaternary structure of RNA polymerase.